USAGE: extract_fastq_barcodes_from_header.py input_reads.fastq barcode_reads.fastq
This depends on biom version >= 2.1.5, < 2.2.0 and vsearch >= 1.7.0.
Please note that all of this is highly experimental. I'm keeping these notes as I work with this approach. For published work, I still recommend using standard pipelines, such as those in QIIME 1.9.1.
$ biom --version biom, version 2.1.5 $ vsearch --version vsearch v1.7.0_osx_x86_64, 16.0GB RAM, 8 cores